Although the Scottish and English parliaments were initially allies in the Wars of the Three Kingdoms, they did not remain so for the entire conflict. Differences in approaches to religion eventually came to the fore with the rise in power and influence of an Independents faction in the English Parliament, in particular its dominance of the New Model Army which alarmed the still Presbyterian-dominated Scottish Parliament. This was not what Scotland's Presbyterian commissioners had envisioned when they signed the Solemn League and Covenant along with their English counterparts. Thus there came a gradual realisation among some Covenanting Scots that a rapprochement or engagement with the King was perhaps the only way to achieve the "true religion" throughout Britain. This idea was hotly contested in Scotland. Only a few were willing to act on such a proposal when the so-called Engagers, unable to persuade the whole Covenanting movement of the wisdom of their strategy, decided they would show their compatriots the way through action rather than words. They invaded England in 1648 without the approval of the Scottish Parliament or General Assembly. However, the Duke of Hamilton proved to be a poor general and was easily defeated by the English parliamentary forces at the Battle of Preston. After the defeat of the Engagers the opposing Kirk Party seized control of the government in Scotland, with the result that from this point on more power was held by Presbyterian ministers than by Presbyterian nobles such as the Earl of Argyll. Not surprisingly, with the declining power and influence of the moderately Royalist Presbyterians and the rise of the more militantly Covenanter Kirk Party, the Scottish government became even more overtly and rigidly Presbyterian. Those who had opposed engaging with the King in 1648 were now effectively governing Scotland. However, even the most militant of Covenanters realised that the English Parliament was never going to enact the Westminster Confession and that the only chance of their Presbyterianism being instituted throughout Britain was through its acceptance by the King. Thus it was that on 23 June 1650 that Charles II landed in Scotland at Garmouth in Moray and by prior agreement, despite his Anglican and Roman Catholic sympathies, signed on his arrival the 1638 National Covenant and 1643 Solemn League and Covenant before being proclaimed King of Scots. This infuriated the English Parliament's Council of State who decided on a pre-emptive invasion of Scotland. Sir Thomas Fairfax, the Army's commander, disagreed with this strategy against the Scots Covenanters, who he saw as Protestant brethren and resigned; his generalship being taken by Oliver Cromwell. John Lambert was made Sergeant Major General and appointed as the Army's second-in-command.

As Cromwell led his army over the border at Berwick-upon-Tweed in July 1650, the Scottish general, Sir David Leslie, continued his deliberate strategy of avoiding any direct confrontation with the enemy. His army was no longer formed of the battle-hardened veterans of the Thirty Years' War who had taken the field for the Scots at the Newburn and the Marston Moor. Many of them had perished during the Civil War and the ill fated 1648 invasion of England. Far more had left active service after the former event, some even leaving for Swedish or French service once more. This meant that a new army had to be raised and trained by the remaining veterans. It eventually comprised some 12,000 soldiers,[1] outnumbering the English army of 11,000 men.[2] Though the Scots were well armed, the pressure of time meant they were poorly trained compared with their English counterparts, all of whom had served with Oliver Cromwell for years. Leslie chose therefore to barricade his troops behind strong defensive works around Edinburgh and refused to be drawn out to meet the English in battle. Furthermore, between Edinburgh and the border with England, Leslie adopted a scorched earth policy thus forcing Cromwell to obtain all of his supplies from England, most arriving by sea through the port at Dunbar.

Whether in a genuine attempt to avoid prolonging the conflict or whether because of the difficult circumstances he found himself in, Cromwell sought to persuade the Scots to accept the English point of view. Claiming that it was the King and the Scottish clergy who were his enemies rather than the Scottish people, he wrote to the General Assembly of the Kirk on 3 August famously pleading, "I beseech you, in the bowels of Christ, think it possible you may be mistaken." This plea, however, fell on deaf ears.

By early September, the English army, weakened by illness and demoralised by lack of success, began to withdraw towards its supply base at Dunbar. Leslie, believing that the English army was retreating, ordered his army to advance in pursuit. The Scots reached Dunbar first and Leslie positioned his troops on Doon Hill on the eastern edge of the Lammermuir Hills,[5] overlooking the town and the Berwick Road, which was Cromwell's land route back to England. Cromwell wrote to the governor of Newcastle:

We are upon an engagement very difficult. The enemy hath blocked up our way at the pass of Copperspath, through which we cannot get without almost a miracle. He lieth so upon the hills that we know not how to come that way without great difficulty; and our lying here daily consumeth our men, who fall sick beyond imagination.

However, the Scots army, commissioned and funded by the Committee of Estates and Kirk representing the Scottish Parliament and the Church of Scotland,[7] manoeuvred itself into a new position, a move that turned out to be a major tactical blunder. Eager to curtail the mounting cost of the campaign, the ministers of the Kirk in attendance are said to have put Leslie under great pressure to press on with an attack. On 2 September 1650, he brought his army down from Doon Hill and approached the town, hoping to secure the road south over the SpottBurn in preparation for an attack on Cromwell's encampment. Witnessing Leslie's men wedge themselves between the deep ditch of the Spott Burn, and the slopes of the Lammermuirs behind them, Cromwell quickly realised that here was an opportunity for him to turn the tables on the Scots. He knew that an attack on the Scottish right flank would leave the left flank unengaged and that a successful push against the right would roll back the latter. On observing the Scots manouevring into their new positions, he is said to have exclaimed, "The Lord hath delivered them into our hands!"[8]

The Major-General [Lambert] and myself coming to the Earl of Roxburgh's House [Brocksmouth House], and observing this posture, I told him I thought it did give us an opportunity and advantage to attempt upon the Enemy. To which he immediately replied, That he had thought to have said the same thing to me. So that it pleased the Lord to set this apprehension upon both of our hearts, at the same instant. We called for Colonel Monk, and showed him the thing: and coming to our quarters at night, and demonstrating our apprehensions to some of the Colonels, they also cheerfully concurred.

That night, under cover of darkness, Cromwell stealthily redeployed a large number of his troops to a position opposite the Scottish right flank. Just before dawn on 3 September, the English troops, shouting their battle cry "The Lord of Hosts!", launched a surprise frontal attack on the Scots, while Cromwell engaged their right flank. Soldiers in the English centre and on the right caught Leslie's men unawares but were held at bay by the long pikes of their Scottish opponents. The right flank of the Scots, however, with less freedom to manoeuvre, was pushed back under the weight of superior English numbers until its lines started to disintegrate. Cromwell's horse then clashed furiously with the Scottish cavalry and succeeded in scattering them. Observing this disaster, the rest of the Scottish army, hopelessly wedged between the Spott or Brox Burn and Doon Hill, lost heart, broke ranks and fled. Cromwell's secretary Rushworth wrote:

I never beheld a more terrible charge of foot than was given by our army, our foot alone making the Scots foot give ground for three-quarters of a mile together.

In the rout that followed, the English cavalry drove the Scots army from the field in disorder.[11] Cromwell reported to Parliament that the "chase and execution" of the fleeing Scots had extended for eight miles.[12]

Cromwell claimed that 3,000 Scots were killed.[3] On the other hand, Sir James Balfour, a senior officer with the Scottish army, noted in his journal that there were "8 or 900 killed".[3] There is similar disagreement about the number of Scottish prisoners taken: Cromwell claimed that there were 10,000,(Cromwell said in his letter to Parliament that he had dismissed 5,000 men because they were Starved, sick or wounded. (Ref:Thomas Carlyle, Letters and speeches)[3] while the English Royalist leader, Sir Edward Walker put the number at 6,000, of which 1,000 sick and wounded men were quickly released.[3] The more conservative estimates of the Scottish casualties are borne out by the fact that, the day after the battle, Leslie retreated to Stirling with some 4,000-5,000 of his remaining troops.[3]

In his post-battle report to the Speaker of the English Parliament, Cromwell described the victory as "...one of the most signal mercies God hath done for England and His people...".[13] As a result of the destruction of the Scottish army, he was able to march unopposed to Edinburgh and quickly occupied the Scottish capital, although Edinburgh Castle held out until the end of December. The prisoners taken at Dunbar were force-marched south towards England in order to prevent any attempt to rescue them. The conditions on the march were so appalling that many died of starvation, illness or exhaustion. By 11 September, when the remnants arrived at Durham Cathedral where they were to be imprisoned, only 3,000 Scottish soldiers were still alive.[14] If Sir Edward Walker's statement is correct, that 6,000 prisoners were taken and 5,000 of them were marched south,[3] then 2,000 captives perished on the way to Durham.

Of the estimated 5,000 Scottish soldiers that began the march southwards from Dunbar, over 3,500 died either on the march or during imprisonment in Durham Cathedral,[15] more than the total number killed on the battlefield. In Arthur Heslerig's letter to parliament on 2 October, He says that he received 3,000 prisoners at Durham and says that the prisoners had not been 'told' (counted) at Berwick. Of the 1,400 survivors, the majority were eventually transported as indentured labourers to English colonies in New England, Virginia and the Caribbean.[16][a][b] After formally accepting the Solemn League and Covenant, Charles was finally crowned King in Scotland on 1 January 1651.

In September 2015, archaeologists from the University of Durham announced that after 18 months work they had concluded that skeletons found in mass graves near Durham Cathedral were the remains of Scottish soldiers taken prisoner after the battle.[19] The bodies had first been discovered in 2013 during building work of a new cafe for the University’s Palace Green Library, on the City’s UNESCO World Heritage Site.[20] The archaeological evidence appeared to show that the bodies had been tipped into a mass grave with no signs of ceremony.[21]

^One of these men was Dr. Patrick Napier [1]. Although Durham Cathedral offered a degree of shelter, the English failed to provide their prisoners with adequate food or fuel.(this may be an untrue statement. Heslerig claimed that he provided food and fuel for the prisoners in the Cathederal and the Castle, which doubled as a hospital) Even at Dunbar, the men were in a starved state. By the time they got to Heslerig, they were almost all suffering from dysentery and many were in the sort of condition that Japanese prisoners of war were in. Just like WWII doctors found it nearly impossible to feed the concentration camp victims, so everything that Heslerig tried was unsuccessful.Ref:Heslerig's letter to parliament 2nd October 1650) Heslerig's letter also refers to Cromwell's wish that the prisoners be marched to Liverpool and Chester and thence to Southern and Western Ireland. Possibly as soldiers, but more probably as settlers. The prisoners were of great value to Cromwell and Heslerig would not have crossed Cromwell in his demand for decent treatment for the prisoners.[17] For a time, the prisoners kept warm by burning all of the woodwork in the Cathedral with the notable exception of Prior Castell's Clock in the South Transept. It is thought that they left the clock alone because it bore a carved thistle, an emblem of Scotland. The prisoners did, however, take the opportunity to revenge themselves on the tombs of the Neville family, beheading their effigies and most of the statuary in the Cathedral. Lord Ralph Neville had commanded part of the English army which had defeated the Scots at the Battle of Neville's Cross in 1346 on the outskirts of Durham City.

^[18] A Letter From Sir Arthur Hesilrige, To the Honorable Committee Of The Councel Of State For Irish and Scotish Affairs at White Hall, Concerning the Scots Prisoners Gentlemen, I Received your Letter dated the Twenty sixth of October, in that you desire me, That Two thousand three hundred of the Scotch Prisoners now at Durham or elswhere, able and fit for Foot Service, be selected, and marched thence to Chester and Liverpool, to be shipped for the South and West of Ireland, and that I should take special care not to send any Highlanders. I am necessitated upon the receipt of this, to give you a full accompt concerning the Prisoners: After the Battel at Dunbar in Scotland, my Lord General writ to me, That there was about Nine thousand Prisoners, and that of them he had set at liberty all those that were wounded, and, as he thought, disabled for future Service, and their Number was, as Mr Downing writ, Five thousand one hundred; the rest the general sent towards Newcastle, conducted to Berwick by Major Hobson, and from Berwick to Newcastle by some Foot out of that Garison, and the Troop of Horse; when they came to Morpeth, the Prisoners being put into a large walled Garden, they eat up raw Cabages, Leaves and Roots, so many, as the very seed and the labor, at Four pence a day, was valued by sufficient men at Nine pounds; which Cabage, as I conceive, they having fasted, as they themselves said, near eight days, poysoned their Bodies; for as they were coming from thence to Newcastle, some dyed by the way-side, and when they came to Newcastle, I put them into the greatest Church in the Town, and the next morning when I sent them to Durham, about Sevenscore were sick, and not able to march, and three dyed that night, and some fell down in their march from Newcastle to Durham, and dyed; and when they came to Durham, I having sent my Lieutenant Colonel and my Major, with a strong Guard both of Horse and Foot, and they being there told into the great Cathedral Church, they could not count them to more then Three thousand; although Colonel Fenwick writ to me, That there were about Three thousand five hundred, but I believe they were not told at Berwick and most of those that were lost, it was in Scotland, for I heard, That the Officers that marched with them to Berwick, were necessitated to kill about Thirty, fearing the loss of them all, for they fell down in great Numbers, and said, They were not able to march; and they brought them far in the night, so that doubtless many ran away. When I sent them first to Durham, I writ to the Major, and desired him to take care, that they wanted not any thing that was fit for Prisoners, and what he should disburse for them, I would repay it. I also sent them a daily supply of bread from Newcastle, and an allowance equal to what had been given to former Prisoners: But their Bodies being infected, the Flux encreased amongst them. I sent many Officers to look to them, & appointed that those that were sick should be removed out the cathedral Church into the Bishops Castle, which belongs to Mistris Blakiston, and provided Cooks, and they had Pottage made with Oatmeal, and Beef and Cabages, a full Quart at a Meal for every Prisoner: They had also coals daily brought to them; as many as made about a hundred Fires both day and night, and Straw to lie upon; and I appointed the Marshal to see all these things orderly done, and he was allowed Eight men to help him to divide the coals, and their Meat, Bread and Pottage equally; They were so unruly, sluttish and nasty, that it is not to be believed; they acted rather like Beasts then Men, so that the Marshal was allowed Forty men to cleanse and sweep them every day: But those men were of the lustiest Prisoners, that had some small thing given them extraordinary: And these provisions were for those that were in health; and for those that were sick, and in the Castle, they had very good Mutton Broth, and sometimes Veal Broth, and Beef and Mutton boild together, and old Women appointed to look to them in the several Rooms: There was also a Physitian which let them Blood, and dressed such as were wounded, and gave the sick Physick and I dare confidently say, There was never the like care taken for any such Number of prisoners that ever were in England. Notwithstanding all this, many of them dyed, and few of any other Disease but the Flux; some were killed by themselves, for they were exceeding cruel one towards another. If a man was perceived to have any Money, it was two to one but he was killed before morning, and Robbed; and if any had good clothes, he that wanted, if he was able, would strangle him, and put on his clothes: And the Disease of the Flux still encreasing amongst them, I was then forced, for their preservation, if possible it might be, to send to all the next Towns to Durham, within four ot five miles, to command them to bring in their Milk, for that was conceived to be the best Remedy for stopping of their Flux, and I promised them what Rates they usually sold it for at the Markets, which was accordingly performed by about Threescore Towns and places, and Twenty of the next Towns to Durham continue still to send daily in their Milk, which is boiled, some with Water, and some with Bean flower, the Physitians holding it exceeding good for recovery of their health. Gentlemen, You cannot but think strange this long preamble, and to wonder what the matter will be; in short its this, Of the Three thousand prisoners that my Officers told into the Cathedral Church at Durham, Three hundred from thence, and Fifty from Newcastle of the Sevenscore left behinde, were delivered to Major Clerk by order from the Councel, and there are about Five hundred sick in the Castle, and about Six hundred yet in health in the Cathedral, the most of which are in probability Highlanders, they being hardier then the rest, and other means to distinguish them we have not, and about Sixteen hundred are dead and buried, and Officers about Sixty, that are at the Marshals in Newcastle. My Lord General having released the rest of the Officers, and the Councel having given me power to take out what I thought fit, I have granted to several well-affected persons that have Salt-works at Sheels, and want Servants, Forty, and they have engaged to keep them to work at their salt-pans; and I have taken out more about Twelve Weavers, to begin a Trade of Linnen cloth like unto the Scotch-cloth, and about Forty Laborers. I cannot give you on this sudden a more exact Accompt of the prisoners, neither can any Accompt hold true long, because they still dye daily, and doubtless so they will, so long as any remain in Prison. And for those that are well, if Major Clerk could have believed that they had been able to have marched on foot, he would have marched them by Land; for we perceive that divers that are seemingly healthy, and have not all been sick, suddenly dye, and we cannot give any reason of it, onely we apprehend they are all infected, and that the strength of some holds it out till it seize upon their very hearts. Now you fully understand the condition and the number of the Prisoners, what you please to direct, I shall observe, and intend not to proceed further upon this Letter, until I have your Answer upon what I have now written. I am, Gentlemen, Your affectionate Servant, Art: Hesilrige Octob, 31, 1650 By the end of October, cold, malnutrition and disease had resulted in the deaths of another 1,600 of the Scottish soldiers. The bodies of many of those who died were buried in a mass grave in the form of a trench running northwards from the Cathedral. The location of their remains was then forgotten for almost three centuries until rediscovered by workmen in 1946. There is no permanent memorial to these soldiers and it is suggested that they had received neither Christian burial nor blessing. Their story is briefly told in the Cathedral guidebook. In 1993 the Cathedral approved in principle a request by the Scottish Covenanters' Memorials Association to erect a suitable memorial or plaque. A campaign properly to respect and remember the 'Dunbar Martyrs' was launched at the end of 2007, aiming at least to gain a Christian blessing for the dead and an adequate memorial at the burial site or even possible exhumation of the remains for reburial in Scotland (Dunbar Martyrs Campaign 2009). On 30 November 2011, St Andrew's Day, a memorial plaque was dedicated in the cathedral (Unwin 2011)